VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 29 2009 - 03:47:08 CST

On Sat, 2009-11-28 at 22:59 -1000, JT wrote:
> Hi all,

hi jeff,

> I just noticed some unexpected behavior when coloring a protein by
> position (radial). I colored the entire cartoon protein using
> position (radial). This generated a very nice image with the protein
> color smoothly blending from blue on one side to white in the middle
> to red on the other side. Then, another representation containing
> just a few residues (drawn as licorice) was added and also colored by
> position (radial). Since these residues were located on the 'red
> side' of the protein, I expected the color of this representation to
> remain red. However, it was actually colored blue and white. I did

have you checked, if you can achieve a consistent coloring by setting
the "Color Scale Data Range" in the Trajectory tab of the second rep
to the numbers found in the first rep?
color scale based reps by default have their own (automatic) range,
but it can be adjusted to have consistent coloring. never tried this
on position data, though...

cheers,
    axel.

> not check, but maybe the 'position' is based only on the atoms in the
> representation selection. Anyway, I'm not sure if adjusting the
> behavior to match my expectation would be an improvement or an
> unnecessary (and unwanted) complication. I just wanted to point it out.
> Good day,
> Jeff Tibbitt 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.